Weird Coincidence
by Dark Phoenix 13X
Summary: Lit AU sorta GGAlias fic. See full summary inside.
1. Prologue

**Title: **Weird Coincidence

**Note:** This is a sorta Gilmore Girls/Alias crossover but none of the Alias characters are in it.

**Summary:** AU: What if Jess had been subjected to a CIA programme when he was 6 years old because Jimmy was (and still is) a CIA operative and because of that program he would make a valuable agent. Liz, his mother, knows nothing of this since Jimmy made up an excuse as to why he and Jess would be gone for 6 months, after that he disappeared. What if Rory was subjected to the same program at 5 by her father Christopher (also a CIA agent) who did so without Lorelai knowing. Lorelai having had an car accident and was in a coma for 6 months in which time Christopher took care of Rory until her mother recuperated. Both Rory's and Jess's memory of those 6 months have been erased or in any way blocked from them. Also both Lorelai and Liz do not know of Chris or Jimmy's involvement in the CIA. Both Jimmy and Chris were not CIA when they were with Lorelai and Liz in high school.

**Spoilers:** everything up to season 5, just to be safe.

**Note2:** Story starts in end Season 3, after Jess left for California to find his father. There is no Sasha Jimmy is a single guy living in an apartment while still working for the CIA. Chris has quit the CIA (before he asked Lorelai to marry him and she refuses) and is now a regular guy.

**Disclaimer: **Don't own them, so don't sue.

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Prologue**

**LA 2004 (end school year), Jimmy's apartment, afternoon**

Jess stands nervously in front of the door trying to act that he was nervous about this decision. He raised his hand and knocked at the door.

"Hold on" the voice of Jimmy Mariano sounded from the other side.

"I don't care what it takes, George. I want to know who else he told about my son." Jimmy said in his cell phone as he opened the door and stared shocked at Jess standing there with a duffel bag over his shoulder. "I'm going to have to call you back George" Jimmy said before he hung up and still stared in the disbelief that his son was actually standing here in front of him. His CIA training kicked him and he quickly pulled his son in side and looked at both sides of the hallway to see anyone suspicious, when seeing no one he closed the door and stared at his son.

"Jess" Jimmy said for the first time since Jess got there. "What are you doing here?"

"Hey dad, nice to see you too." Jess replied.

Jimmy raised his hand to the back of his head and scratched it as he said "Sorry, it's nice to see you too Jess. It's just…unexpected."

"Yeah well so was you showing up in Stars Hollow, after how long? 12 years?" Jess told him.

"Look I'm sorry I showed up and dropped that bombshell on you like that. But if you're here to yell at-" Jimmy started but Jess cut in.

"I'm not, it's just…I have nowhere else to go. I failed school, Luke kicked me out, my mom doesn't want me around and I just thought you might…let me stay here just until I got a job and made enough money to get a place on my own." Jess told him.

Jimmy scratched the back of his head again obviously conflicted on what to do, part of him wanted his son to stay with him, and another part finds it too dangerous for both of them. "Uhm are you sure Luke kicked you out, I mean that doesn't sound like Luke."

"I had a deal with Luke, I graduate I can stay. I don't want to go back to school next year so Luke said I couldn't live with him." Jess said then added "if you don't want me here just say so, I'll find somewhere else to-" this time Jess was cut off.

"It's not that, it's just…complicated." Jimmy sighted as his mind raced to come up with a solution. "Why aren't you finishing school?" he asked Jess to buy some time.

"You didn't. Guess it's genetic." Jess told him.

"Actually I did, a little late but I did." Jimmy informed him.

"Why?" Jess asked him feeling slightly stupid.

"Well before your mom didn't know this but while we were in New York I took some night classes after work and eventually I graduated and got a better job. This job…it was dangerous and no t just to me…" Jimmy stops considering how much to tell him without actually telling his son what he did for a living. "They offered me a promotion here in LA" he lied "so I left your mother a note which I guess you know about and I send the two of you some money every month."

"Mom never told me about a note or any money she would get from you." Jess told him.

Jimmy sighted "I guess she was trying to protect you from getting hurt by me the way she got hurt." He told his son.

"So you left us for a promotion?" Jess asked unconvinced.

"Yes" Jimmy lied "and a bunch of other reasons. I don't know if you remember or not but your mom and me were constantly fighting. It seemed like the right thing to do. Get out of the way." Jimmy half lied half said truthfully.

"Ok," Jess said unconvinced but let it go and decided to ask "So what did you mean about "who else he told about my son" you said on the phone earlier? Where you talking about me or do I have a half brother I should know about?" Jess asked.

"Just some guy from work who overheard me telling a friend about visiting you and I don't like my personal life public knowledge." Jimmy lied to his son.

"Yeah sure, me too" Jess told him accepting this lie although it felt wrong to him somehow; he had always been good at reading people.

Jimmy smiled uncomfortably while still thinking about Jess staying here. Finally he reasoned that while staying here might be dangerous he would at least be able to keep an eye on him here.

"So what do you do?" Jess asked trying to sound casual through the uncomfortableness between him and his father.

Jimmy caught off guard because of his new decision to let his son stay here "Huh…Oh, I work at Jennings Aerospace, here in town. I sell airplane parts." He said knowing the building was the cover for SD-6, the organisation which was a branch of the Alliance. The Alliance was a criminal organization founded by 12 members who had all gone rogue after the fall off the Soviet Union. He worked as a double agent for the CIA while giving the information about SD-6.

"Ok" Jess said not wanting to comment on how boring that sounded to him "so I can stay or should I go?" he asked after a minute of silence between them.

"Oh, yeah sure." Jimmy said still feeling weird about his son moving in with him and also guilty over starting this new relationship with his son with lies. Also the thought that if he could actually forge some kind of bond with his son that it would have to be temporarily because he wasn't about to pull his son into the craziness that was his life.

**Stars Hollow begin 2004 (begin school year), Dragonfly inn, afternoon**

"Calm down honey, I'm sure no one is following you. Just stay in your dorm room with Paris until I get there, ok?" Lorelai said through the phone.

"Lorelai" A familiar voice said causing Lorelai to look in the direction it came.

"Chris" Lorelai said surprised but relieved he was there.

Through the phone _"Dad is there?"_ Rory asked her mother.

"Uhu" Lorelai Gilmore managed to get out before saying "I'll be there soon hun, try to stay calm and don't let anyone in you or Paris don't know." She held up a finger to Chris showing she'd get to him in a minute.

"_Alright mom, can you ask dad to come?"_ Rory asked.

"I'll ask him, bye sweetie."

"_Bye mom, and thanks"_ Rory said.

"Sure" Lorelai said before hanging up the phone. "Michel, can you cover for me?" She asked him.

"Sure, just hurry back" Michel said not arguing with her because he was secretly worried about Rory as well but not admitting that to anyone.

"Thanks" Lorelai said to Michel then to Chris just as she pulled him with her outside "I don't know why you are here Chris but Rory thinks someone is following her and she doesn't want to call campus security because it would look like she's some crazy girl worried over nothing so she wants us to come and reassure her she is wrong and no one is following her."

"Oh God" Chris said as Lorelai and he were outside. He ran over to his Volvo, "get in" he almost ordered her. Lorelai both worried and scared by the sudden change in Chris did what he said and soon after Chris had started the engine and sped off.

"Chris?" Lorelai asked shocked and worried but this time Chris held up a finger and pulled out his cell phone and speed dialled someone.

"Yeah, it's me. You were right….No she's with me it's my daughter….Yes I'm heading over there right now….I'd appreciate that…..Ok, thanks." Chris hung up and Lorelai was about to ask what was going on again when Chris gave her the one minute finger again.

"Rory honey it's you father. Listen, if you Sherry shows up there don't let her in, ok?" Chris told her.

"_Dad, why? What's going on?"_ Rory asked her voice unnerving.

"I'll explain when I get there, I promise. Just stay in your dorm until your mom and I get there." Chris told her.

"_Dad, no tell me what's going on!"_ Rory demanded.

"Rory, please just do what I say. We'll be there soon and I'll explain everything, I promise." Chris told her.

"_Ok"_ Rory said.

"Thank you, we'll be there soon. I love you" Chris said.

"_I love you too dad. See you soon"_ Rory told him as she hung up.

"Bye" Chris said and sighted as he hung up and put his phone away as he focussed on the road and increased his speed slightly and at the same time trying to figure out how to start explaining all this to Lorelai.

"Alright Chris I have been more then patient and you are really freaking me out so talk!" Lorelai ordered him.

Chris sighted glanced at Lorelai before back the road "I know, and I appreciate it is just kind off hard to begin telling you. Especially since I promised myself you and Rory would never get hurt by this, and that this part of my life was over." Chris paused for a moment and took a deep breath as he began his story.

"After you left your parents house and took off with Rory and told me we weren't going to be a family I was lost. Then one day a person approached me, told me he worked for the US government and that they were interested in offering me a job. I said no at first but I started to wonder if I could do it be an agent for the US government, I called them and asked why me, they said I fit a profile and when I said yes I started working for them. Mostly with paper stuff, then after 2 months I asked to test for agent training. I became a CIA agent. It was fun, and working for them gave my life meaning. I kept it a secret from you and Rory to protect you; I also tried to limit my contact with you. Finally a few years ago, a few weeks before I came to Stars Hollow and proposed to you I had been captured. I managed to escape but the whole time I kept thinking of you and Rory. So when I finally managed to escape after a week and a half of torture and questions I managed to escape. I caught the woman who had me captive and then I quit the CIA. After I recuperated enough came to see you and Rory." Chris told her and paused again letting Lorelai absorb all of this.

"Chris, if this is some kind of prank-" Lorelai started.

Chris looked at her with a dead serious expression on his face before saying "I'm sorry to get the two of you involved in all of this."

"Involved in what? Is someone after Rory because of your connection to the CIA?" Lorelai asked.

"Sort of, it's complicated. This morning I found out Sherry was planted to be with me. That even Gigi isn't mine but she was impregnated because she was losing me to you and they wanted us to be apart. Sherry was, is an agent working for the woman I took into custody before I left the CIA. Last night the woman escaped while being transferred and one of the security camera's showed it was Sherry that helped her escape. I was on business and drove straight to your inn when I found out hoping I was worrying about you and Rory for nothing. But if Rory is already being watched…I asked the CIA just now to keep a look out at anything suspicious at Yale. She'll be fine Lore, I promise I'm not going to let anything happen to her or you." Chris tried to reassure Lorelai who looked still confused, very shocked and most of all worried about her daughter.

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What do you think so far?


	2. Chapter 1 – You fit a profile

**Chapter 1 – You fit a profile**

**Note:** Paris and Asher never happened but she did break up with Jamie two days prior this.

**Rating: **R for the violence.

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LA 2004, Park**

Jess was sitting on a bench reading a book when man sat beside him on the bench. Jess looked up from his book and to the man in a suit who was looked at him or at least seemed to, it was hard to tell with the dark sunglasses covering his eyes.

"I have an offer for you." The man said and Jess took another glance at the suit and then returned his eyes to the book he was reading saying "Whatever it is, I'm not interested."

The man observed him for a few seconds thinking _'what the hell is going through his head ordering me to bring this punk kid into the fold. Oh well'_ out loud he said "Jess Mariano, I'm Tom Gest. I work for the Central Intelligence Agency. I'm here to offer you a job to come work for us."

Jess looked away from the book with disbelief and looked back at Tom "what? Is this some kind of stupid prank or something because you can't be serious."

"The CIA doesn't pull…pranks." Tom said looked at the young man.

"So then it is a mistake. You've got the wrong guy." Jess told him.

"Jess Mariano, son of James Mariano and Elizabeth Danes/Mariano nephew of one Luke Danes. Recently flunked out of high school left his girlfriend in another state…" Jess who listed with a bored expression on his face despite the bad feeling he had about this. And the slight interest he felt. He opened his mouth to say something in his defence about leaving Rory but the CIA agent continued ignoring his attempt to speak "…then moved in with your father Jimmy Mariano who works at Jennings Aerospace." Tom paused and then repeated "The CIA does not make mistakes, either." He added.

"Did Lorelai put you up to this?" Jess asked finding it all still difficult to believe the guy was for real.

"Which Lorelai are we talking? Your ex-girlfriend? Her mother or her mothers' mother-in-law.

Jess took a few seconds to process everything "So what does the CIA what with such a failure like me?" Jess asked in a chipper voice which dripped of sarcasm.

"Like I said, we are offering you a job." Tom repeated ignoring the sarcasm.

"Yeah I got that, but why me?" Jess asked.

"You fit a profile" Tom answered before giving him his card. "Think about it Jess." He then said before leaving Jess alone with the card and his thoughts.

**Yale 2004, Rory and Paris dorm room**

There was a knock on the door and Rory shot Paris a panicked look.

"Who's there!" Paris demanded.

"Paris it's me, open up!" Jamie's voice said from behind the door.

"It's Jamie. What is he doing here, with someone stalking us?" Paris asked Rory.

Rory shrugged and said "he's your ex-boyfriend ask him."

"I will not, I am still not talking to him. You're the one being so paranoid about someone stalking us, you ask him." Paris told Rory.

"Fine, I will." Rory replied then said loudly through the door "What are you doing here Jamie? You know Paris is not speaking to you."

"Rory? Open up, please. I have to talk to Paris. Explain…." Jamie started but Paris cut him off.

"There is nothing to explain Jamie, you lied to me. You said you were at your mothers but you were at some girls house." Paris voice said harshly.

"Can't we talk about this inside, everyone is looking at me out here." Jamie asked.

"No!" was Paris simple answer.

"Fine Paris I lied to you I didn't go to my mother but to my old friend Ashley who works at a juwel store where I bought you something that I was picking up there. Would you please open the door now Paris?"

"So why couldn't you just say you were going to Ashley's to pick up something you bought instead of lying to me and saying you were at your mothers?" Paris demanded.

"Oh for crying out, fine…Paris will you marry me?" Jamie asked.

Paris looked shocked and when she looked at Rory she noticed the same expression on her face. Walking over to the door she left the chain on and opened it to reveal Jamie on one knee and a small crowd behind him. Paris still didn't say anything but before she had a chance to a man from the crowd behind Jamie suddenly dropped dead after soft std noise and a woman with a gun with a silencer walked up to them and aimed at Paris before noticing Rory looking from below Paris head and then said "Come willingly or they all die" Rory's eyes widened but before she could do anything Jamie had stood up stepped in front of the two women.

Before Jamie could speak a bullet was fired and Jamie fell forwards dead. Paris screamed and Rory's instincts took over and pushed Paris away from the door unto the floor before looking fanatically around for a weapon, finding a knife she took it in her hand before looking around needing a plan. Rory grabbed Paris and dragged her to her room "Be quiet" she ordered her and closed the door. She looked around the room knowing she had seconds before the door would come crashing down.

The door flew open to reveal an empty room the female agent sent to capture Rory Gilmore her soft sobbing from the room Paris was in and smiled walking towards the door gun ready.

Rory softly sneaked up behind the female from her hiding place behind the door when it flew open. She pressed the knife against the female's back and said "drop it."

The female agent froze cursing herself for not checking the room more thoroughly before going after the obvious. She threw her gun away and at the exact moment when Rory was distracted she spun around and grabbed the knife from Rory who then let instinct again take over and before she knew it she had kicked the knife out of the female's hand and assumed a fighting stance unfamiliar to her yet familiar to her somehow. Then before the female would attack her again a familiar voice said "You killed my boyfriend." Paris said holding the knife against the female agents back in the same way Rory had moments ago.

The female agent swallowed as fear she had not tasted in a long time began to creep up on her. "Drop it kid, or your best friend will suffer the same fate as your boyfriend." Sherry said as she had a gun aimed at Rory.

Paris looked from Rory to Sherry and stepped back dropping the knife to the floor.

The female agent smiled "thanks Sherry." She said before she fetched her earlier discarded gun and aimed it at Paris.

A shot was fired and Sherry put a hand to her stomach which was bleeding before she fell over. "Drop it Megan" Chris voice said in a ordering tone.

Megan glared at him as she pointed the gun at his daughter "No my sweet ignorant little Chris. You drop it or your daughter gets one in the head."

Chris glared at her but as he was about to put the gun down Paris had somehow picked the knife up and looked at Rory who was looking from Megans' gun to her father to the gun on the ground near a very dead Sherry. She nodded to Paris who threw the knife at Megan just as Chris had dropped his gun and Rory jumped towards Sherry's gun and rolled over unto her back aiming it for Megan was about to shoot Paris for a knife that was stuck in her side. Rory fired the gun and Megan screamed before looking at Rory then at Chris who was reaching for his gun and then she dropped a smoke bomb and when the smoked cleared she was gone.

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So what do you think? 


	3. Chapter 2 – Difficult decisions

haven't updated this one in a while, sorry for the long wait here is the next chapter.**

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**Chapter 2 – Difficult decisions**

**Yale 2004, Rory and Paris dorm room**

Rory stared at where the woman whom she learned was Megan had been, a feeling of unreal keeping her from crawling in a corner or break down. Paris however was now sitting besides Jamie's dead body crying.

Rory looked at her father who looked at Sherry then looked concerned at her, Rory looked blankly back at him not sure how to react. Her father being here with a gun shooting Sherry, she couldn't deal with right now. She walked over to Paris and kneeled beside her placing a hand on her back. Paris gripped unto Rory and continued to sob into her.

Lorelai Gilmore stormed in moments later causing Rory and Paris to break apart and Rory raising the gun she still had in her hand pointing it at her mother. Seeing her mother she dropped the gun out of her hand suddenly scared of it. It fell to the ground and Rory jumped up and ran into her mothers embrace finally letting her emotions out and crying in her mothers arms.

Chris looked at the two with sadness in his eyes, feeling responsible for all the death and pain caused here today. Sighing he pulled out his mobile phone and dialled a number.

Lorelai was shocked to see her daughter point a gun at her but soon recovered from that shock when Rory was in her arms hugging her tight and crying.

After a while Rory had calmed down and pulled away from her mother with new resolve she looked at her father who was just hanging up a mobile phone.

"What the hell is going on dad!" she demanded to know.

"You better sit down for this hun" her mother said worried.

"I'd rather stand. What the hell was Sherry doing here with a gun? Who was this Megan? Why were you here with a gun? And what the hell happed to me? How come I dropped in a fighter stance I don't know? How do I know how to use a weapon? What did Sherry and Megan want with me? Tell me!" Rory ordered her father.

"Alright, I worked for the CIA. That's why I haven't been much in your life or haven't kept promises I made. A while ago I arrested Megan and she went to prison, until Sherry broke her out. Sherry turns out to have been a plant, someone to get to close to me and get information from me. Also to keep my contact with you and your mom limited. Because I was the one who put Megan in custody she wanted to kidnap you for revenge. When Lorelai was in a coma I subjected you to an experimental program called project Christmas. I wanted you to be able to take care of yourself if the situation called for it. It is how you knew how to handle a gun, fight, how to survive. I then had someone suppress your memories of those 6 months and when Lorelai regained consciousness you nor she knew anything about it. I'm sorry I did this without both your knowledge but I wanted you to be able to take care of yourself if something like this should ever happen to you." Chris told her daughter.

"You…programmed me to be a spy?" Rory said shocked.

"No, I helped you be able to take care of yourself should something dangerous happen to you. You can do and be whoever you want to be." Christopher told her.

"No I can't, because now people like Megan know who I am, who mom is. They will come after us again." Rory told her.

"I'm sorry, I was doing what I thought was right. I can arrange for you both to go into the witness protection program." Chris told them.

"Chris" Lorelai said feeling to confused and emotional by everything she learned about him, her daughter, their lives to really process everything. "I don't want to leave my life. I like my life. I finally have my own inn. I have friends here, Sookie, Luke. I don't want to leave." She told him.

"And I have Lane, Paris, grandma, grandpa, Yale. I can't leave Yale." Rory told him.

"But it's not safe…unless no." Chris said quickly dismissing his thought.

"What Chris?" Lorelai asked.

"You're not going to like this. And I don't want that kind of life for you or our daughter." Chris told her.

"Tell us, dad." Rory told him.

"Unless I stayed in Stars Hollow to look after your mom while you Rory join the CIA so you'll learn to take care of yourself."

"My daughter…our Rory in the CIA!" Lorelai told Chris angrily.

"I told you, you wouldn't like it. But it's the only way I see that will allow her to continue her life here without assigning CIA operatives to watch her for the rest of her life." Chris told the mother of his only child.

"Then we'll go into witness protection, Rory is not going to join the CIA." Lorelai said determined.

"I can just become an annalist mom. I wouldn't have to go into the field or do dangerous missions." Rory told her.

Lorelai shot her an shocked look that said how-can-you-even-consider-this!

"That could work, but you would be trained as field operative just so you know how to defend yourself." Chris told her.

Lorelai shot Chris an angry look "She is not joining the CIA. I will not allow it."

"Mom, it's the only way we'll be able to continue our lives and be prepared for any more possible attacks." Rory told her mother as calmly as she could.

Lorelai hugged her daughter "I don't want to lose you"

"You won't." Rory promised her.

**LA 2004, Jimmy's place**

Jess sat on the couch reading but he couldn't stop wondering about the CIA guy in the park, they wanted him. Could he do it, could he really become an CIA agent? Yeah that would be the day, Jess Mariano a CIA agent. He thought and dismissed and focussed back on his book. Not much later he was reading the card the CIA guy had given him.

Jess distracted himself with work the rest off the week but at the end of the week he laid on his bed looking at the card. "I'm just going to call and see what happens. I could use the money." He told himself as he picked up Jimmy's phone and dialled the number.

**New Haven 2004, Safehouse**

Rory layed awake in her bed thinking about the events of this day and her joining the CIA. Her dad told her she'd have to pass some tests. Her mind wondered to Jess and she wondered what he was doing and how it would be if she was still his girlfriend. How would Jess react to her joining to CIA or her almost dying or being kidnapped today. Tears made her way down her cheeks as her heart ached for him to hold her in his arms.

She got out of bed and walked to the window and looked at the full moon and stars in the sky "I love you Jess, wheverever you are. For the first time I'm glad you're not in my life anymore. That you're safe somewhere else. I miss you, tough. As much as I try not to I can't help myself. I'll do my best to take care of myself, for my mom, my dad, my friends, myself and you. I'll become the best CIA agent there is. I'll protect not just myself, but all of you as well." she then vowed feeling a renwed strength and determinationinside her as she pictured her friends, her family, her Jess in danger from terorists. "I'll protect you" she told them before getting back into her bed and picked up her copy of "Howl". She had been alowed some to bring some of her stuff.

She opened the book after she crawled back into bed and turned on the light at her nightstand and started to read, ocasionaly smiling as she read Jess's notes in the margin.

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review please. 


	4. Chapter 3 – Living the life of a spy

Sorry for the long wait, I'm just busy with too many fics at once. As usual, lol. Anyways thaks for the nice reviews, here is another chapter with a nice Lit scene in it :D

Nick.**

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**Chapter 3 – Living the life of a spy**

**Stamford, September 2006, Rory and Paris's apartment**

Years passed and Rory became a amazing CIA agent while still attending Yale. She somehow managed to combine school, work and her social life together. Speaking of her social life, Rory now shared an apartment with Paris. Paris had eventually moved on and was now dating a guy named Doyle. She and Rory had moved to Stamford when it suited them bother better for work their jobs. Paris managed to land herself an internship and eventually a job at New York's Presbyterian hospital. While the CIA office in New York was where of course Rory's job was. Although getting up early to get to school or New York was a not something they both liked they had gotten used to it.

Besides Paris, Marty became another great friend of hers. But with Marty she hid her CIA life. The only persons knowing about it were Paris, her mom, dad and of course the people she worked with. Although she was considered the best agent Rory did not have that many friends at her work, there was her partner Sima Yi. Yi was a nice unmarried Chinese guy in his late thirties who talked a lot. He had been Rory's trainer together with Christopher who stopped by every now and then to check on how his daughter was doing. Yi had eventually became her partner.

Besides Yi there was Rory's commanding officer Joe McDowell. Joe was also nice and joked a lot but could be very strict when the situation called for it. Joe is in his early 40, is married and has 3 children. The last person Rory was somewhat friends with was the tech guy. Mitchell Guevara was an unmarried, smart, conceited, cared about the equipment he invented. He also seemed to be only nice to women. He was dating Vicky Sweets who kept him on a tight leash.

Besides work and school Rory visited Stars Hollow when she could to talk with her parents. Her parents who after a long time of being just friends finally got together about a year and a half ago and got married about 9 months ago. Rory didn't talk much about the dangers of her work to her mom. She just talked about the cities she'd been, how beautiful some things looked, how lucky she was to get her daily amount of coffee into her system sometimes on a mission. She talked somewhat more about the dangers to her father but still not everything. She hated keeping things from them but knew it was for the best. Then there was Lane, they called each other every now and them to keep each other updated on their lives. Rory hadn't told her about what she really does for a living. Just that she works at a bank. Lane eventually married Dave and is currently together with Lorelai pregnant. While Lorelai prepares the world for her first son Lane is preparing the world for her daughter.

When Rory found out her best friend and mom were both pregnant she was happy for them, but something ached inside her as well. She hadn't had a serious relationship in over 2 years. She started her final year at Yale last week but in all that time she had not had a serious relationship. Although she was asked out and went on dates it didn't become serious. Sometimes she found reason why the relationship wouldn't work, at other times she sabotaged them by keeping the person at distance. Never letting anyone into her heart. She told herself and Paris at times it was because of her job. The real reason however was in California. Rory had looked up where he lived when he came to see her a year and a half ago. She'd broken his heart as well as her own that day.

Rory sighed as she replayed that day in her head.

_Flashback_

_**Stars Hollow, 2005, Luke's diner,**_

_Rory gulped her coffee down and sighed contently. "No matter where I go, Luke's coffee remains the best." She told her mom who was sitting across her at the table._

_Lorelai smiled at her daughter but didn't say anything but glanced nervously at the curtains every now and then._

"_What is it mom?" Rory asked calmly._

"_I uh, well…nothing. What makes you think there is something?" Lorelai asked._

"_Because I know you and I'm trained in this kinda thing. You keep glancing at the curtain. Is someone up there I should know about?" Rory asked._

_Lorelai looked at her daughter trying to convince her nothing was wrong then sighed and broke "Jess showed up yesterday afternoon." She told her daughter._

_Rory looked at her "Oh" she said processing the fact Jess was very close._

"_I'm sorry I didn't tell you I just…I know how much he upsets you and I like your visits and don't want them to be ruined by him." Lorelai told her just as Jess appeared from behind the curtain and froze starring at Rory._

_Rory forced a convincing smile "I'm fine mom. What we had is ancient history. I'm over it." She told her mother in a steady convincing tone not having noticed Jess._

_Jess looks at the two then tells Luke "I'm going for a walk."_

_Rory quickly turns around fear of him having hurt what she just said and shock to have him actually be here. But when she did all she saw was his retreating form out of the diner._

_Rory looked back at her mother her eyes pleading for her approval to go after him. She then blinked confusion now visible over her features. As she remained seated struggling with buried emotions Lorelai's voice pulled her out of her thoughts._

"_Go." Rory heard and looked up at her mother._

_She was silent not sure what to say or do until she grabbed her jacket and told her mother "I'll be right back."_

_**Stars Hollow, 2005, Bridge,**_

_Rory wasn't sure where she was to look for him when the memory popped into her head and her feet already started walking towards the bridge._

_As the bridge came into view she could make out a figure sitting on it, she silently walked closer thinking of what to say to him._

_Jess felt her approach, even without all his SD-6 training he would know it was her. He looked out over the water before turning his head and looked at her._

"_Hi." Rory said sitting down next to him._

"_Hi" Jess replied._

"_Oh my God Jess what happened?" Rory demanded when she could see the partly uncovered bruise on his face. Her hand reached up and wiped the concealer away revealing a large bruise._

_Jess pulled away from her "It's nothing." He told her starring back out at the water as he silently cursed himself for not covering it up better. It must have been being back at Luke's old apartment that threw him off his game and made him miss a spot._

"_It's not nothing, there is a large bruise on your face." Rory told him annoyed he was shutting her out again._

"_I'm fine, I got hit with a ball again." He told her._

_Rory looked at him knowing he was lying and then suddenly realizing something "no you're not. And you weren't back when you had a black eye when you showed up at my grandmothers." She told him._

"_Fine I wasn't, why do you care? I thought we were ancient history? I thought you were over me?" Jess asked her._

"_Jess" Rory said not knowing exactly what to say to him but wanting to say something._

"_I still love you, you know." Jess suddenly dropped at her and looked her in the eyes to see her reaction as well as to show her he was serious._

"_Jess" Rory said again but was cut of when his mouth suddenly covered hers and she was lost once again in his warm magnetic touch. She responded needing him, all her fears and trouble melted away as their lips touched and her tongue invited herself in his mouths dancing with his. Needing his taste. Her hands wrapped themselves around him, pulling his closer, needing more of him. She gasped for breath when the pulled apart for oxygen before looking at each other, seeing the desire in each others' eyes and crashing their lips together once more._

_As Rory began to lay down pulling Jess with her on top of her. Jess pulled away and looked into her eyes "I love you." He told her and Rory froze then smiled as she looked into his eyes and put a hand on his cheek. Without saying anything she turned them over and began to unbutton his shirt saying "I know."_

_Jess stopped her by taking her by placing his hand over hers and with his other raised her head so her eyes met his. "Do you love me?"_

"_I…I can't." Rory told him remembering her work the dangers, the danger she would put Jess in if she told him that. He needed her and she needed him but it couldn't be more, they couldn't be more. She would not have him hurt because of her life. She took a deep breath preparing herself to push Jess away, for good out of her life. For his own safety._

_But before she could say anything Jess was out from under her and on his feet buttoning his shirt saying "Yeah, maybe this wasn't the best idea." He told her._

'_Oh' Rory thought hurt but pushing it aside and saying "You're probably right."_

"_I shouldn't have kissed you. I'm sorry." Jess then told her._

'_I'm not' Rory's thought then she pushed the thought aside "It's alright, I think we both enjoyed it…right?"_

_Jess looked at her and smiled slightly saying "I know I did."_

_Rory blushed but smiled at him before asking "So who did this to you?"_

_Jess looked at her trying to compose an answer that would be convincing and somewhat true. "Some men attacked me, wanted information I couldn't give them." Jess told her eventually._

"_What kind of information?" Rory asked gently as she softly traced the bruise on his face with her right hand. Their eyes interlocked and the air crackled around them._

"_If I couldn't tell them I can't tell you." Jess told her "Just that it's work related." He breathed trying not to lose control and kiss Rory again._

_Rory struggled to contain herself and eventually dropped her hand and took a step back. "And what kind of job do you have Jess?" she asked him._

"_I got a job at Credit Dauphine, it's a bank back in LA" Jess told her._

"_Huh, really? I got a job at a bank too. In New York." Rory told him surprised._

"_New York?" Jess asked surprised. "You graduated Yale already?"_

"_No, I'm still going to Yale. I got an apartment with Paris in Stamford." Rory told him._

"_Paris huh, she pregnant too?" Jess asked._

_Rory laughed "No, she is seeing someone though. His name is Doyle…it took a her a long time to get over Jamie." She finished sadly._

"_What happened to Jamie?" Jess asked._

"_He uh…" Rory started uncomfortable "he was killed." She told him._

"_Oh, sorry." Jess told her._

"_It's ok, it was a long time ago." Rory replied then changed the subject "So how is life in California other then being beat up by men?"_

"_It's ok…I miss you though." He then told her._

_Rory looked at him struggling with words. "I can't." she told him._

"_Why?" Jess asked._

"_Because…because I'm involved with someone." She lied._

"_No you're not." Jess told her._

"_What? I am too." Rory told him._

"_Are not." Jess told her._

"_Am too." Rory replied._

"_Are not." Jess replied._

"_Am- Why are we arguing like 5 year olds? I told you I'm seeing someone just accept that I've moved on." Rory told him annoyed that he was seeing right through her lie._

"_Because I know you Rory. I know I hurt you but you can trust me now. You can rely on me." Jess told her._

"_I…" she wanted so bad to give him to kiss him, let him hold her in his arms and feel safe again but she couldn't. She couldn't let him in her life, he may be in her heart forever but he wouldn't be in her life. It was too dangerous, he could get hurt. Or worse. An image of Jamie suddenly falling to the ground dead appeared before her and she took another step back "I can't."_

"_What are you so afraid of?" Jess asked not understanding. "Please Rory, give me another chance." He pleaded._

_She shook her head fighting her heart will and said "I said I can't Jess. Get over it already."_

_Her own harsh words shocked her as well as him and she saw his heart break through his eyes as he took a step back then walked away. Rory fought the urge to go after him and sat back down at the bridge starring out at the water as she whispered "it's for the best."_

**_Stars Hollow, 2005, Crap Shack_**

"_Lore, Rory?" Christopher called when he got home._

_Rory sat up right on her bed wiping the tears from her face "here!"_

_Christopher opened Rory's door to see his daughter sitting in her chair reading a book. "hey" Chris said approaching._

_Rory put the book away hoping he wouldn't notice her slightly puffy red eyes "hi."_

_But Chris hadn't been in the CIA doing nothing "Ror? What happened?" he asked._

_Rory opened her mouth to explain but instead a sob came out as her last resolve broke and she flung her arms around her father, sobbing into him._

"_Hey, Ror?" Chris said putting his arms around her letting her soak his shirt._

_After a few minutes Rory pulled away and wiped her tears away "I'm sorry." She apologized._

"_Don't be sorry, just tell me what happened." Chris told her._

_Rory was silent for a moment before looking her father in the eye saying "I broke his heart. He told me he loved me and I just pushed him away. I couldn't say it back. I couldn't let him into my life." She told her father wiping new tears from her face._

"_Who?" Chris asked confused._

"_Jess. Who else, I've never let anyone else get too close. I've never loved anyone else as much as I still love him. I tried not to, I tried to move on but every time I try I push them away. I couldn't give anyone else my heart, I already gave it away. And now I broke it along with his." She sat down on her bed and hugged her pillow close to her._

"_Jess? Not the Jess who broke your arm?" Chris asked her._

"_Fractured my wrist, it was an accident dad. Get over it already." Realizing she just used thee exact same words she used not too long ago to Jess. Rory gasped immediately said "I'm sorry dad, I didn't mean-" _

"_I know." Chris interrupted her "So you love this Jess. Why did you push him away? If he loves you too he would not mind you working for the CIA. It is not as if he would be going on the missions with you."_

"_But he'd still be part of it, part of my life. What if someone decides to take revenge on me and kill him. It'd be my fault, I don't want to be responsible for any more death and causing other people pain." She told her father thinking of Jamie and Paris._

_Chris sighed and sat down on Rory's bed next to her "Rory, you are not responsible for your friend Paris and Jamie's death. If anyone should be it'd be the women who attacked you all. You have to move past this and move on, let yourself be happy. Don't deny yourself love because you're sacred of what might happen. Think about what will happen if you don't allow anyone to get too close. You're going to end up alone and miserable." He told her taking his hand in his. "There are no guaranties nothing will happen but you have to take a chance. This Jess will forgive you if something should happen but if it doesn't and he finds out why you wouldn't give him another chance he would never forgive you for that."_

_Rory looked at her father and hugged him._

**_LA, 2005, Jess's apartment,_**

_Rory paced around the front door then froze when she heard a noise from behind it and when Jess opened the door there was no one._

_Jess shrugged thinking he must have imagined it and closed the door._

_Outside Rory looked up at the window with sad eyes and new determination 'it's for the best.' She thought to herself._

_Jess looked out of his window and froze, he was seeing someone he couldn't have possible be seeing. He blinked and she was gone 'if nearly dying on my latest mission wasn't bad enough, now I'm going crazy. Rory did the right thing back in Stars Hollow. I couldn't have stand to lie to her every day about what I really do.'_

_Jess's pager went off and he walks over to it looks at it **Grimes - 911 –**_

'_Great, another mission…well at least it will get my mind of her.' He thought to himself._

_End Flashback_

**LA, 2006, Jess's apartment,**

Jess sighed as he looked at the picture of Rory he had in his copy of Ayn Rand's "The Fountainhead". His life had changed so much, so much because of her and his job at SD-6.

He had an apartment now, 1 jobs, friends and even school. One job was of course with a secret branch of the CIA called SD-6. School was something his boss Grimes didn't like he had but he wasn't giving it up. Although surprised that he decided to go to college after his father made him finish high school he was a student at UCLA, his major being in English.

At school Jess had met Matthew and later Chris. The three of them became friends and are planning to open a publishing company when they graduate from UCLA. Although Jess only told them he worked at a bank and took trips every now and then. Matthew having been Jess's friend the longest was used to it. Chris still complains to Jess about working too much at the bank. Lying to them Jess didn't like but the rules about telling another person about his job were made pretty clear to him when he accepted the job.

His job at SD-6 got him to be the partner of Rhonda Johnson, a black unmarried women in her later thirties. She was tough, hard to get to know, but a good friend once you were friends with her. Which Jess being her partner for some time had managed to become. Besides Rhonda there was their tech girl Diana Wilkins, she was amazingly smart, had a photographic memory, was nice, in her late twenties, unmarried, slightly geeky and babbled a lot when she was nervous, which seemed whenever when she was around other people.

Jess's boss was a man in his late forties named Olivier Grimes, he had been very nice to Jess ever since he started working with SD-6. Jess's trainer had been a man named Charles Bloom but when he was killed on a mission a year after Jess's training began Grimes had taken over as Jess's mentor. Jess respected the guy and he had grown close to him, seeing him as a father figure. Jess had been to his home, met his wife Rachel Grimes. Rachel was also obsessed with books which didn't make it hard for Jess to become friends with her.

As for Jess's contact with his biological father Jimmy, well it had come to a rocky halt somehow. Jess had given him a chance to connect but it somehow had ended with him canceling dinner and Jess feeling abandoned once more. So he stopped calling and contact stopped between the two stopped.**

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**Hope you liked that, let me know by reviewing.


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